rs1356266

Variant names:

• chr12-39009779-C-T
• rs1356266

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.535 in 151,926 control chromosomes in the GnomAD database, including 24,704 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.53 (24704 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81103 AN: 151806 Hom.: 24641 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.480

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.535 AC: 81232 AN: 151926 Hom.: 24704 Cov.: 31 AF XY: 0.531 AC XY: 39416 AN XY: 74228

African (AFR) AF: 0.850 AC: 35247 AN: 41480

American (AMR) AF: 0.458 AC: 6973 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1331 AN: 3468

East Asian (EAS) AF: 0.441 AC: 2274 AN: 5152

South Asian (SAS) AF: 0.349 AC: 1682 AN: 4820

European-Finnish (FIN) AF: 0.463 AC: 4872 AN: 10532

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27511 AN: 67922

Other (OTH) AF: 0.485 AC: 1026 AN: 2114

Alfa AF: 0.486 Hom.: 3498

Bravo AF: 0.554

Asia WGS AF: 0.436 AC: 1519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.52
PhyloP100		0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1356266; hg19: chr12-39403581;